From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 22 Jun 2016 11:54:43 +0000 (+0100)
Subject: Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
X-Git-Tag: Release_2_10_0~161
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f2b86d72de53efb41fd1d57335fb0a61a9efe3ea;hp=f7c9911a43d7b85a3f0097eb99825b73f3a95713;p=jalview.git

Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
---

diff --git a/examples/appletDeployment.html b/examples/appletDeployment.html
index 87953df..0301225 100644
--- a/examples/appletDeployment.html
+++ b/examples/appletDeployment.html
@@ -18,10 +18,10 @@
 -->
 
 
-<div id="view_decorated" name="view_decorated"  style="margin:8px; padding:10px; border: 2px solid red; text-align:center; display:none;"><b>Click <a href="index.html#appletDeployment"> here</a> to view decorated page</b></div>
+<div id="view_decorated" name="view_decorated"  style="margin:8px; padding:10px; border: 2px solid red; text-align:center; display:none;"><b>Click <a href="index.html#appletDeployment"> here </a> to view decorated page</b></div>
 
 <!-- content start -->
-<h2><a name="appletDeployment"/>Notes on applet deployment</h2>
+<h2 name="appletDeployment"> Notes on applet deployment</h2>
 <table width=80% border="1">
   <tr><th colspan="2" align="center">Required Dependency Downloads</th></tr>
   <tr>
@@ -46,13 +46,30 @@
   </tr>
 </table>
 
-        <ul>
+<p>The snippet below shows a mininmal code for embeding Jalview applet into a web page.    
+<pre><code>
+&lt;applet code="jalview.bin.JalviewLite" width="756" height="560" archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar"&gt;
+	&lt;param name="permissions" value="sandbox" /&gt;
+	&lt;param name="file" value="plantfdx.fa" /&gt;
+	&lt;param name="features" value="plantfdx.features" /&gt;
+	&lt;param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF" /&gt;
+	&lt;param name="showFullId" value="false" /&gt;
+	&lt;param name="embedded" value="true" /&gt;
+	&lt;param name="linkLabel_1" value="Uniprot" /&gt;
+	&lt;param name="linkUrl_1"	value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$" /&gt;
+	&lt;param name="linkLabel_2" value="EMBL-EBI Search" /&gt;
+	&lt;param name="linkUrl_2"	value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$" /&gt;
+	&lt;param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp" /&gt;
+&lt;/applet&gt;
+</code></pre> 
+
+For more information and advanced options, see the <a href="javascript:doSubmit('appletParameters')"><strong>applet parameters page</strong></a>, and other documentation in the links to the left. 
+  <ul>
           <li>Package all your data files into a single (or multiple) zip / jar 
             files. This is very useful to reduce download time of large data files. 
             The applet archive tag can take multiple entries separated by commas, 
             eg<br>
-            <pre>&lt;applet code=&quot;jalview.bin.JalviewLite&quot;<em><strong> 
-            archive=&quot;jalviewApplet.jar, mydata.zip&quot;</strong></em>&gt;
+            <pre>&lt;applet code=&quot;jalview.bin.JalviewLite&quot;<em><strong> archive=&quot;jalviewApplet.jar, mydata.zip&quot;</strong></em>&gt;
             </pre></li>
           <li> Use Jalview for input to a HTML form. For an example of how to 
             code this using Javascript, click <a href="javascript:doSubmit('formComplete')">here</a>. 
diff --git a/examples/applets.html b/examples/applets.html
index 34118b8..02d1d09 100644
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -22,19 +22,13 @@
 
 <!-- boiler plate link to alternate demopage -->
 <div style="width: 100%">
-<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
-<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-14.2.14_2015.06.11.jar">JmolApplet.jar</a>
-</p></div>
 </div>
-</div>
-
 <!-- content template start -->
 
 <p align="left">
 <h2>JalviewLite Button Examples</h2>
 Try out JalviewLite by pressing one of the buttons below.<br/>
- For more information on how to use the applet in your website, see the <a href="javascript:doSubmit('appletParameters')"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
+ For more information on how to use the applet in your website, see the <a href="javascript:doSubmit('appletDeployment')"><strong>applet deployment,</strong></a> <a href="javascript:doSubmit('appletParameters')"><strong>applet parameters,</strong></a> and other documentation in the links to the left.</p>
 <p>&nbsp;</p><div align="center">
   <p align="center">
     <h2>Ferredoxins, chloroplast precursor related UniRef50
diff --git a/examples/embedded.html b/examples/embedded.html
index aa67325..d4e00f9 100644
--- a/examples/embedded.html
+++ b/examples/embedded.html
@@ -23,9 +23,6 @@
 <!-- boiler plate link to alternate demopage -->
 <div style="width: 100%">
 <div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
-<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-14.2.14_2015.06.11.jar">JmolApplet.jar</a>
-</p></div>
 </div>
 </div>
 
diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html
index f629312..1ecff58 100644
--- a/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@ -260,11 +260,7 @@ jmolInitialize("","JmolApplet-14.2.14_2015.06.11.jar");
   modeltofiles+="1gaq.txt";
 </script> 
 <div style="width: 100%">
-<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
-<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-14.2.14_2015.06.11.jar">JmolApplet.jar</a>
-</p></div>
-</div>
+
 </div>
 
 <!-- content template start -->
diff --git a/examples/formComplete.html b/examples/formComplete.html
index 91d94f8..dc651fb 100644
--- a/examples/formComplete.html
+++ b/examples/formComplete.html
@@ -24,9 +24,7 @@
 <!-- boiler plate link to alternate demopage -->
 <div style="width: 100%">
 <div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
-<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-14.2.14_2015.06.11.jar">JmolApplet.jar</a>
-</p></div>
+
 </div>
 </div>
 
diff --git a/examples/javascriptLaunch.html b/examples/javascriptLaunch.html
index e161ad6..47f60e8 100644
--- a/examples/javascriptLaunch.html
+++ b/examples/javascriptLaunch.html
@@ -21,12 +21,7 @@
 
 <!-- boiler plate link to alternate demopage -->
 <div style="width: 100%">
-<div style="width:35%; align:left; float:right;">
 
-<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
-<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-14.2.14_2015.06.11.jar">JmolApplet.jar</a>
-</p></div>
-</div>
 </div>
 
 <!-- content template start -->
diff --git a/examples/linkedapplets_ng.html b/examples/linkedapplets_ng.html
index 0449c0b..4df08fc 100644
--- a/examples/linkedapplets_ng.html
+++ b/examples/linkedapplets_ng.html
@@ -22,9 +22,7 @@
 <!-- boiler plate link to alternate demopage -->
 <div style="width: 100%">
 <div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
-<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-14.2.14_2015.06.11.jar">JmolApplet.jar</a>
-</p></div>
+
 </div>
 </div>